I think each FTO will need to explain the specific benefits of their courses, which won't necessarily arise solely from their location. A dose of critical thinking is helpful to the wannabe in sorting through the feature/benefit lists that each will communicate to you. Finally, features others think are meaningful may not be important to you and vice versa. The key is to do enough research to inform your decision well.
JAA training is JAA training. Period. The standards one must meet to pass the theory exams and check rides are the same on both sides of the Atlantic.
JAA does not allow the entire fATPL training to be done in the USA though. The IR check ride must be done in European airspace, which also necessitates a portion of the flying be done in Europe so the student is familiar enough with the airspace, radio calls, etc. to pass the check flight. Each US JAA FTO will probably have an EU location or training partner to provide some or all of the IR training and skills test.